I used to go 40+ miles without any cycling shorts and the way to minimize the pain was to change my riding position a lot. Getting out of saddle a lot and stuff like that. I used to do this for like 2 years with decent success and only the last 10 miles or so would be real unconformable as I got used to it.

I never got any saddle sores but I was getting fed up with discomfort towards the end of the rides.

So recently,,,, I got some shorts,,,, and now its just a breeze and I feel like I can go 50 more miles with no discomfort.

I feel like riding without shorts on long rides has thought me a lot about fitting my self and how to minimize discomfort.